The authors aimed to evaluate the factors affecting clinical outcomes of cystine stone disease in children and to understand the change in disease management over time. Between January 1991 and September 2017, the demographic and clinical data of pediatric patients with documented cystine stone disease were retrospectively analyzed. Patients with at least 12-month follow-up were included. Disease management and clinical outcomes were compared between the first and second 35 patients managed during the study's time frame. A total of 70 patients were included. The female to male ratio was 30/40. The mean age and follow-up period was 29.8 +/- 40.1 months and 106.5 +/- 56 months, respectively. The mean initial procedure number to treat the first stone episode was 2.4 +/- 1.6. Single stone and single affected site were significant predictors for stone clearance. Overall, patients underwent a mean of 5.5 procedure during their follow-up. Recurrence was detected in 71.4% (50/70) of patients. Residual fragments and non-compliance to medical treatment after the initial intervention were significant predictors for recurrence within shorter interval period. 31.4% (22/70) of patients had renal atrophy during follow-up. They were older at the initial diagnosis and had average urine pH lower than 7.5. The first 35 patients had more open procedures. Still, they had more recurrence rate and tend to have more renal atrophy. As a conclusion, cystine stone disease has a recurrent course in children. Stone and fragments entirely removed (SaFER) concept with all minimally invasive methods available and strict follow-up should be the basis for any management plan.